Ecosyste.ms: Issues

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GitHub / khanlab/snakebids issues and pull requests

#337 - Fix typo in BidsValidator plugin

Pull Request - State: closed - Opened by pvandyken 10 months ago
Labels: bug

#336 - Overhaul `snakebids create`

Pull Request - State: closed - Opened by pvandyken 10 months ago - 6 comments
Labels: enhancement

#335 - Extension of `BidsComponent.filter` api

Issue - State: open - Opened by pvandyken 10 months ago

#334 - Add deprecation mechanism to old pybidsdb vals

Pull Request - State: closed - Opened by pvandyken 11 months ago
Labels: bug

#333 - `pybids_db_dir` was eliminated without warning, causing migration issues

Issue - State: closed - Opened by pvandyken 11 months ago - 2 comments

#332 - Refactor filter_list to use RegexContainer

Pull Request - State: closed - Opened by pvandyken 11 months ago
Labels: maintenance

#331 - Add poetry lock check

Pull Request - State: closed - Opened by pvandyken 11 months ago - 1 comment
Labels: maintenance

#330 - Update dependencies and pyright version

Pull Request - State: closed - Opened by pvandyken 11 months ago
Labels: maintenance

#329 - Port documentation changes

Pull Request - State: closed - Opened by pvandyken 11 months ago
Labels: skip_changelog

#328 - Update docs dependencies

Pull Request - State: closed - Opened by pvandyken 11 months ago - 1 comment

#327 - Port hotfixes from 0.9.x

Pull Request - State: closed - Opened by pvandyken 11 months ago
Labels: bug

#326 - Fix version fetching in readthedocs build

Pull Request - State: closed - Opened by pvandyken 11 months ago - 1 comment
Labels: bug, documentation

#326 - Fix version fetching in readthedocs build

Pull Request - State: closed - Opened by pvandyken 11 months ago - 1 comment
Labels: bug, documentation

#325 - HOTFIX Fix pybidsdb path resolution

Pull Request - State: closed - Opened by pvandyken 11 months ago
Labels: bug

#325 - HOTFIX Fix pybidsdb path resolution

Pull Request - State: closed - Opened by pvandyken 11 months ago
Labels: bug

#324 - Implement Bids Spec files

Pull Request - State: closed - Opened by pvandyken 11 months ago - 1 comment
Labels: maintenance

#323 - Fix mistaken comparison of BidsEntity to str sets

Pull Request - State: closed - Opened by pvandyken 11 months ago
Labels: bug, skip_changelog

#323 - Fix mistaken comparison of BidsEntity to str sets

Pull Request - State: closed - Opened by pvandyken 11 months ago
Labels: bug, skip_changelog

#322 - Drop support for Python 3.7

Pull Request - State: closed - Opened by pvandyken 11 months ago - 1 comment
Labels: breaking

#322 - Drop support for Python 3.7

Pull Request - State: closed - Opened by pvandyken 11 months ago - 1 comment
Labels: breaking

#321 - SnakeBidsApp Assumes filters are present

Issue - State: open - Opened by pvandyken 11 months ago
Labels: bug

#320 - Update scipy constraints for py3.8

Pull Request - State: closed - Opened by kaitj 11 months ago - 3 comments
Labels: maintenance

#320 - Update scipy constraints for py3.8

Pull Request - State: closed - Opened by kaitj 11 months ago - 3 comments
Labels: maintenance

#319 - Scipy dependency

Issue - State: closed - Opened by kaitj 11 months ago
Labels: bug

#319 - Scipy dependency

Issue - State: closed - Opened by kaitj 11 months ago
Labels: bug

#317 - fixing small virtual env activation typo in tutorial.md

Pull Request - State: closed - Opened by ataha24 about 1 year ago
Labels: documentation

#317 - fixing small virtual env activation typo in tutorial.md

Pull Request - State: closed - Opened by ataha24 about 1 year ago
Labels: documentation

#316 - Update cookiecutter

Pull Request - State: closed - Opened by kaitj about 1 year ago - 4 comments
Labels: maintenance

#316 - Update cookiecutter

Pull Request - State: closed - Opened by kaitj about 1 year ago - 4 comments
Labels: maintenance

#315 - Drop Support for Py37

Issue - State: closed - Opened by pvandyken about 1 year ago - 1 comment
Labels: breaking

#315 - Drop Support for Py37

Issue - State: closed - Opened by pvandyken about 1 year ago - 1 comment
Labels: breaking

#314 - Allow Booleans in filter lists

Pull Request - State: closed - Opened by pvandyken about 1 year ago - 2 comments
Labels: bug

#313 - Use PEP 621-based pyproject.toml in snakebids create

Issue - State: closed - Opened by tkkuehn about 1 year ago - 3 comments

#312 - Add plugin reference page to docs

Pull Request - State: closed - Opened by kaitj about 1 year ago
Labels: documentation

#311 - Plugins page in docs

Issue - State: closed - Opened by kaitj about 1 year ago
Labels: documentation

#311 - Plugins page in docs

Issue - State: closed - Opened by kaitj about 1 year ago
Labels: documentation

#310 - Always set SnakeBidsApp.args in run_snakemake

Pull Request - State: closed - Opened by tkkuehn about 1 year ago
Labels: maintenance

#310 - Always set SnakeBidsApp.args in run_snakemake

Pull Request - State: closed - Opened by tkkuehn about 1 year ago
Labels: maintenance

#309 - Boolean CLI filters

Pull Request - State: closed - Opened by tkkuehn about 1 year ago - 1 comment
Labels: enhancement

#309 - Boolean CLI filters

Pull Request - State: closed - Opened by tkkuehn about 1 year ago - 1 comment
Labels: enhancement

#308 - Save more provenance information

Pull Request - State: closed - Opened by tkkuehn about 1 year ago - 9 comments
Labels: enhancement

#307 - Update app creation instructions

Issue - State: closed - Opened by kaitj about 1 year ago - 2 comments
Labels: documentation

#307 - Update app creation instructions

Issue - State: closed - Opened by kaitj about 1 year ago - 2 comments
Labels: documentation

#306 - Update cookiecutter template

Pull Request - State: closed - Opened by kaitj about 1 year ago - 1 comment
Labels: maintenance

#306 - Update cookiecutter template

Pull Request - State: closed - Opened by kaitj about 1 year ago - 1 comment
Labels: maintenance

#305 - Test magic args

Pull Request - State: closed - Opened by tkkuehn about 1 year ago - 3 comments
Labels: test

#305 - Test magic args

Pull Request - State: closed - Opened by tkkuehn about 1 year ago - 3 comments
Labels: test

#304 - `export_sourcedir` plugin

Issue - State: open - Opened by pvandyken about 1 year ago - 1 comment
Labels: enhancement, plugin

#302 - Expect plugins to be callable classes

Issue - State: open - Opened by tkkuehn about 1 year ago - 1 comment

#302 - Expect plugins to be callable classes

Issue - State: open - Opened by tkkuehn about 1 year ago - 1 comment

#301 - Split bids into its own repository

Issue - State: closed - Opened by tkkuehn about 1 year ago - 1 comment

#300 - Add DuplicateComponentError for more precision

Pull Request - State: closed - Opened by tkkuehn about 1 year ago
Labels: maintenance

#300 - Add DuplicateComponentError for more precision

Pull Request - State: closed - Opened by tkkuehn about 1 year ago
Labels: maintenance

#298 - Update README

Pull Request - State: closed - Opened by kaitj about 1 year ago
Labels: documentation

#297 - Raise error on missing `custom_path` and invalid `bids_dir`

Pull Request - State: closed - Opened by kaitj about 1 year ago
Labels: maintenance

#296 - Update pybids_db parameters

Pull Request - State: closed - Opened by kaitj about 1 year ago - 1 comment
Labels: maintenance, deprecation

#296 - Update pybids_db parameters

Pull Request - State: closed - Opened by kaitj about 1 year ago - 1 comment
Labels: maintenance, deprecation

#295 - Make the target easier to override in plugins

Issue - State: closed - Opened by pvandyken about 1 year ago - 1 comment
Labels: enhancement

#294 - Allow builtins as types

Issue - State: closed - Opened by pvandyken about 1 year ago
Labels: enhancement

#293 - Mandatory vs Optional components in `pybids_inputs`

Issue - State: open - Opened by pvandyken about 1 year ago - 2 comments
Labels: enhancement

#293 - Mandatory vs Optional components in `pybids_inputs`

Issue - State: open - Opened by pvandyken about 1 year ago - 2 comments
Labels: enhancement

#292 - Improve implementation of `get()` in `MultiSelectDict`

Issue - State: open - Opened by pvandyken about 1 year ago - 2 comments
Labels: enhancement

#291 - Add BidsValidator Plugin

Pull Request - State: closed - Opened by kaitj about 1 year ago - 4 comments
Labels: enhancement

#291 - Add BidsValidator Plugin

Pull Request - State: closed - Opened by kaitj about 1 year ago - 4 comments
Labels: enhancement

#285 - Implement extension support

Pull Request - State: closed - Opened by pvandyken about 1 year ago - 3 comments
Labels: enhancement

#285 - Implement extension support

Pull Request - State: closed - Opened by pvandyken about 1 year ago - 3 comments
Labels: enhancement

#284 - Implement `BidsPartialComponent`

Pull Request - State: closed - Opened by pvandyken about 1 year ago - 5 comments
Labels: enhancement

#283 - Restrict pybids bug check to python 3.7

Pull Request - State: closed - Opened by pvandyken about 1 year ago - 6 comments
Labels: maintenance

#270 - Why is `pybids_db_dir` commented in the boilerplate config?

Issue - State: closed - Opened by pvandyken over 1 year ago - 1 comment
Labels: maintenance

#270 - Why is `pybids_db_dir` commented in the boilerplate config?

Issue - State: closed - Opened by pvandyken over 1 year ago - 1 comment
Labels: maintenance

#269 - Confusing menagerie of names for pybids database

Issue - State: closed - Opened by pvandyken over 1 year ago
Labels: breaking

#269 - Confusing menagerie of names for pybids database

Issue - State: closed - Opened by pvandyken over 1 year ago
Labels: breaking

#264 - Expose `args` on `SnakeBidsApp` for plugins

Issue - State: closed - Opened by pvandyken over 1 year ago
Labels: enhancement

#264 - Expose `args` on `SnakeBidsApp` for plugins

Issue - State: closed - Opened by pvandyken over 1 year ago
Labels: enhancement

#262 - Deprecate `participant_label` and `exclude_participant_label` args

Issue - State: closed - Opened by pvandyken over 1 year ago - 4 comments
Labels: deprecation, blocked

#259 - BIDS validation

Pull Request - State: closed - Opened by kaitj over 1 year ago - 8 comments
Labels: enhancement

#259 - BIDS validation

Pull Request - State: closed - Opened by kaitj over 1 year ago - 8 comments
Labels: enhancement

#258 - Extend boolean filtering to cli

Issue - State: closed - Opened by pvandyken over 1 year ago - 1 comment
Labels: enhancement

#256 - Automatically create pybidsdb

Issue - State: open - Opened by pvandyken over 1 year ago
Labels: enhancement, plugin

#246 - Versioned `bids` functions

Issue - State: closed - Opened by pvandyken over 1 year ago
Labels: enhancement

#245 - Customizable `bids` function based on spec file

Issue - State: closed - Opened by pvandyken over 1 year ago - 5 comments
Labels: enhancement

#244 - `BidsDataset` advanced component selection

Issue - State: open - Opened by pvandyken over 1 year ago - 1 comment
Labels: enhancement

#244 - `BidsDataset` advanced component selection

Issue - State: open - Opened by pvandyken over 1 year ago - 1 comment
Labels: enhancement

#243 - Implement `BidsPartialComponent`

Issue - State: closed - Opened by pvandyken over 1 year ago
Labels: enhancement

#243 - Implement `BidsPartialComponent`

Issue - State: closed - Opened by pvandyken over 1 year ago
Labels: enhancement

#241 - `BidsDataset.filter`

Issue - State: open - Opened by pvandyken over 1 year ago - 1 comment
Labels: enhancement

#236 - Breaking `BidsDataset` API Changes

Issue - State: open - Opened by pvandyken over 1 year ago
Labels: breaking

#235 - Support `extension` in `bids()` function

Issue - State: closed - Opened by pvandyken over 1 year ago - 1 comment
Labels: bug

#235 - Support `extension` in `bids()` function

Issue - State: closed - Opened by pvandyken over 1 year ago - 1 comment
Labels: bug

#232 - Extending filtering to meta-data

Issue - State: closed - Opened by Bradley-Karat over 1 year ago - 2 comments
Labels: enhancement

#222 - integrate bids validator by default into snake bids

Issue - State: closed - Opened by Remi-Gau over 1 year ago - 5 comments
Labels: enhancement

#222 - integrate bids validator by default into snake bids

Issue - State: closed - Opened by Remi-Gau over 1 year ago - 5 comments
Labels: enhancement

#221 - add an easy way for user to add a README and dataset_description to their output

Issue - State: open - Opened by Remi-Gau over 1 year ago - 6 comments
Labels: enhancement

#219 - Missing `custom_path` when bids_dir invalid should throw error

Issue - State: closed - Opened by pvandyken over 1 year ago
Labels: bug

#216 - `participant_label` applies subject filter to every single component

Issue - State: closed - Opened by pvandyken over 1 year ago - 1 comment
Labels: bug

#206 - Expose snakemake as a script

Issue - State: closed - Opened by pvandyken over 1 year ago - 2 comments
Labels: enhancement, wontfix

#205 - Saving more provenance information

Issue - State: closed - Opened by pvandyken over 1 year ago - 4 comments